My dampners never went bad, but my Ujoint did, and I felt it thumping in the footpegs first. This thumping is more related to on and off the throttle (stressing the driveline).
But thumping can be a wheel bearing too, and the most common one to fail is the single row bearing on the left rear (and I lost that too). See the double row bearing replacement mod on the left rear in Shoptalk. This thumping can also be related to on and off the throttle, but it can also come on at certain lower speeds intermittently, regardless of throttle play. Try tight turns to induce bearing symptoms (squawking/squealing/grinding).
When these things start to go south slowly (as opposed to catastrophically), it can be hard to figure out. Until you do, don't go far from home.
For the bearing, put the bike on the jack and check the wheel for lateral play, or push it fore and aft and feel for movement that shouldn't be there. Spin and listen (maybe with your ear on a long screwdriver).
A little slop in the drive line can be normal, but not too much. You can ride the bike in first slow and just easily goose the throttle a bit (don't overdo this). You're trying to find out if your Ujoint is failing, but hard goosing (the torquey bitch) with a newly failing Ujoint can make it fully fail.
This is about the best how to-on the Ujoint (clicking each picture, blows it up and reveals more information).
http://www.rattlebars.com/mtz/ujoint.htmlOf course, tearing it down in back is the only way to really know what's up. And if you do need a new Ujoint or wheel bearing, that's the only way to fix it.
When I needed a Ujoint, I ordered one (and a shaft, and a pinion cup), but I only needed the Ujoint. I just didn't want to have to wait on parts I might need. If you do need a Ujoint, do yourself a favor and get a new boot. A new one only takes all afternoon to put back on, the old one may take several days (and I poked a hole in my old one anyway trying to force it on; and that meant water inside the driveline, which is a very bad thing).
If it's the wheel left rear wheel bearing, I highly recommend the double row left mod. Your rear brake caliper spacer has to be machined down a bit shorter. A new one is not too spendy ($20), so I ordered one and took it to a shop with the specs for machining, so it was ready when I needed it.
With your low miles, I doubt it's the wheel dampners, but age can always be a factor. The telltale sign here is crumbly rubber under the dampner cover.
The only oil I ever used that reduced gear whine was the 10/40 MC specific Amzoil, but when it went to $13 a quart, I quit using it. A gallon of Shell Rotella T6 is $6 less than two quarts of Amzoil.